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Pepelnjak M, Velten B, Näpflin N, von Rosen T, Palmiero UC, Ko JH, Maynard HD, Arosio P, Weber-Ban E, de Souza N, Huber W, Picotti P. In situ analysis of osmolyte mechanisms of proteome thermal stabilization. Nat Chem Biol 2024; 20:1053-1065. [PMID: 38424171 PMCID: PMC11288892 DOI: 10.1038/s41589-024-01568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
Organisms use organic molecules called osmolytes to adapt to environmental conditions. In vitro studies indicate that osmolytes thermally stabilize proteins, but mechanisms are controversial, and systematic studies within the cellular milieu are lacking. We analyzed Escherichia coli and human protein thermal stabilization by osmolytes in situ and across the proteome. Using structural proteomics, we probed osmolyte effects on protein thermal stability, structure and aggregation, revealing common mechanisms but also osmolyte- and protein-specific effects. All tested osmolytes (trimethylamine N-oxide, betaine, glycerol, proline, trehalose and glucose) stabilized many proteins, predominantly via a preferential exclusion mechanism, and caused an upward shift in temperatures at which most proteins aggregated. Thermal profiling of the human proteome provided evidence for intrinsic disorder in situ but also identified potential structure in predicted disordered regions. Our analysis provides mechanistic insight into osmolyte function within a complex biological matrix and sheds light on the in situ prevalence of intrinsically disordered regions.
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Affiliation(s)
- Monika Pepelnjak
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Britta Velten
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Centre for Organismal Studies (COS) & Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Nicolas Näpflin
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tatjana von Rosen
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Jeong Hoon Ko
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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2
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Prajapati SK, Pathak A, Samaiya PK. Alzheimer's disease: from early pathogenesis to novel therapeutic approaches. Metab Brain Dis 2024; 39:1231-1254. [PMID: 39046584 DOI: 10.1007/s11011-024-01389-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
The mainstay behind Alzheimer's disease (AD) remains unknown due to the elusive pathophysiology of the disease. Beta-amyloid and phosphorylated Tau is still widely incorporated in various research studies while studying AD. However, they are not sufficient. Therefore, many scientists and researchers have dug into AD studies to deliver many innovations in this field. Many novel biomarkers, such as phosphoglycerate-dehydrogenase, clusterin, microRNA, and a new peptide ratio (Aβ37/Aβ42) in cerebral-spinal fluid, plasma glial-fibrillary-acidic-protein, and lipid peroxidation biomarkers, are mushrooming. They are helping scientists find breakthroughs and substantiating their research on the early detection of AD. Neurovascular unit dysfunction in AD is a significant discovery that can help us understand the relationship between neuronal activity and cerebral blood flow. These new biomarkers are promising and can take these AD studies to another level. There have also been big steps forward in diagnosing and finding AD. One example is self-administered-gerocognitive-examination, which is less expensive and better at finding AD early on than mini-mental-state-examination. Quantum brain sensors and electrochemical biosensors are innovations in the detection field that must be explored and incorporated into the studies. Finally, novel innovations in AD studies like nanotheranostics are the future of AD treatment, which can not only diagnose and detect AD but also offer treatment. Non-pharmacological strategies to treat AD have also yielded interesting results. Our literature review spans from 1957 to 2022, capturing research and trends in the field over six decades. This review article is an update not only on the recent advances in the search for credible biomarkers but also on the newer detection techniques and therapeutic approaches targeting AD.
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Affiliation(s)
- Santosh Kumar Prajapati
- Bhavdiya Institute of Pharmaceutical Sciences and Research, Ayodhya, UP, India
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, 33613, USA
| | - Arjit Pathak
- Department of Pharmacy Shri G.S. Institute of Technology and Science, Indore, 452003, Madhya Pradesh, India
| | - Puneet K Samaiya
- Department of Pharmacy Shri G.S. Institute of Technology and Science, Indore, 452003, Madhya Pradesh, India.
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3
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Arar S, Haque MA, Bhatt N, Zhao Y, Kayed R. Effect of Natural Osmolytes on Recombinant Tau Monomer: Propensity of Oligomerization and Aggregation. ACS Chem Neurosci 2024; 15:1366-1377. [PMID: 38503425 PMCID: PMC10995947 DOI: 10.1021/acschemneuro.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
The pathological misfolding and aggregation of the microtubule associated protein tau (MAPT), a full length Tau2N4R with 441aa, is considered the principal disease relevant constituent in tauopathies including Alzheimer's disease (AD) with an imbalanced ratio in 3R/4R isoforms. The exact cellular fluid composition, properties, and changes that coincide with tau misfolding, seed formation, and propagation events remain obscure. The proteostasis network, along with the associated osmolytes, is responsible for maintaining the presence of tau in its native structure or dealing with misfolding. In this study, for the first time, the roles of natural brain osmolytes are being investigated for their potential effects on regulating the conformational stability of the tau monomer (tauM) and its propensity to aggregate or disaggregate. Herein, the effects of physiological osmolytes myo-inositol, taurine, trimethyl amine oxide (TMAO), betaine, sorbitol, glycerophosphocholine (GPC), and citrulline on tau's aggregation state were investigated. The overall results indicate the ability of sorbitol and GPC to maintain the monomeric form and prevent aggregation of tau, whereas myo-inositol, taurine, TMAO, betaine, and citrulline promote tau aggregation to different degrees, as revealed by protein morphology in atomic force microscopy images. Biochemical and biophysical methods also revealed that tau proteins adopt different conformations under the influence of these osmolytes. TauM in the presence of all osmolytes expressed no toxicity when tested by a lactate dehydrogenase assay. Investigating the conformational stability of tau in the presence of osmolytes may provide a better understanding of the complex nature of tau aggregation in AD and the protective and/or chaotropic nature of osmolytes.
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Affiliation(s)
- Sharif Arar
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department
of Chemistry, School of Science, The University
of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Nemil Bhatt
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department
of Internal Medicine, University of Texas
Medical Branch, Galveston, Texas 77555, United States
- Institute
for Translational Sciences, University of
Texas Medical Branch, Galveston, Texas 77555, United States
| | - Rakez Kayed
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
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Yadav H, Jaldhi, Bhardwaj R, Anamika, Bakshi A, Gupta S, Maurya SK. Unveiling the role of gut-brain axis in regulating neurodegenerative diseases: A comprehensive review. Life Sci 2023; 330:122022. [PMID: 37579835 DOI: 10.1016/j.lfs.2023.122022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Emerging evidence have shown the importance of gut microbiota in regulating brain functions. The diverse molecular mechanisms involved in cross-talk between gut and brain provide insight into importance of this communication in maintenance of brain homeostasis. It has also been observed that disturbed gut microbiota contributes to neurological diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and aging. Recently, gut microbiome-derived exosomes have also been reported to play an essential role in the development and progression of neurodegenerative diseases and could thereby act as a therapeutic target. Further, pharmacological interventions including antibiotics, prebiotics and probiotics can influence gut microbiome-mediated management of neurological diseases. However, extensive research is warranted to better comprehend this interconnection in maintenance of brain homeostasis and its implication in neurological diseases. Thus, the present review is aimed to provide a detailed understanding of gut-brain axis followed by possibilities to target the gut microbiome for improving neurological health.
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Affiliation(s)
- Himanshi Yadav
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Faculty of Science, University of Delhi, Delhi, India
| | - Jaldhi
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Faculty of Science, University of Delhi, Delhi, India
| | - Rati Bhardwaj
- Department of Biotechnology, Delhi Technical University, Delhi, India
| | - Anamika
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Amrita Bakshi
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Suchi Gupta
- Tech Cell Innovations Private Limited, Centre for Medical Innovation and Entrepreneurship (CMIE), All India Institute of Medical Sciences, New Delhi, India
| | - Shashank Kumar Maurya
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Faculty of Science, University of Delhi, Delhi, India.
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5
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Mitra S, Munni YA, Dash R, Sadhu T, Barua L, Islam MA, Chowdhury D, Bhattacharjee D, Mazumder K, Moon IS. Gut Microbiota in Autophagy Regulation: New Therapeutic Perspective in Neurodegeneration. Life (Basel) 2023; 13:life13040957. [PMID: 37109487 PMCID: PMC10144697 DOI: 10.3390/life13040957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/18/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
Gut microbiota and the brain are related via a complex bidirectional interconnective network. Thus, intestinal homeostasis is a crucial factor for the brain, as it can control the environment of the central nervous system and play a significant role in disease progression. The link between neuropsychological behavior or neurodegeneration and gut dysbiosis is well established, but many involved pathways remain unknown. Accumulating studies showed that metabolites derived from gut microbiota are involved in the autophagy activation of various organs, including the brain, one of the major pathways of the protein clearance system that is essential for protein aggregate clearance. On the other hand, some metabolites are evidenced to disrupt the autophagy process, which can be a modulator of neurodegeneration. However, the detailed mechanism of autophagy regulation by gut microbiota remains elusive, and little research only focused on that. Here we tried to evaluate the crosstalk between gut microbiota metabolites and impaired autophagy of the central nervous system in neurodegeneration and the key to future research regarding gut dysbiosis and compromised autophagy in neurodegenerative diseases.
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Affiliation(s)
- Sarmistha Mitra
- Department of Anatomy, College of Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, College of Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - Raju Dash
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Toma Sadhu
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chittagong 4000, Bangladesh
| | - Largess Barua
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Md. Ariful Islam
- Department of Pharmaceutical Sciences, North South University, Dhaka 1229, Bangladesh
| | - Dipannita Chowdhury
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Debpriya Bhattacharjee
- Faculty of Environment and Natural Sciences, Brandenburg Technical University Cottbus Senftenberg, D-03013 Cottbus, Germany
| | - Kishor Mazumder
- Department of Pharmacy, Jashore University of Science and Technology, Jashore 7408, Bangladesh
- School of Optometry and Vision Science, UNSW Medicine, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | - Il Soo Moon
- Department of Anatomy, College of Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
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6
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The Role of a Gut Microbial-Derived Metabolite, Trimethylamine N-Oxide (TMAO), in Neurological Disorders. Mol Neurobiol 2022; 59:6684-6700. [DOI: 10.1007/s12035-022-02990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
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7
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TMAO to the rescue of pathogenic protein variants. Biochim Biophys Acta Gen Subj 2022; 1866:130214. [PMID: 35902028 DOI: 10.1016/j.bbagen.2022.130214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.
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8
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Microbial-derived metabolites as a risk factor of age-related cognitive decline and dementia. Mol Neurodegener 2022; 17:43. [PMID: 35715821 PMCID: PMC9204954 DOI: 10.1186/s13024-022-00548-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/30/2022] [Indexed: 02/06/2023] Open
Abstract
A consequence of our progressively ageing global population is the increasing prevalence of worldwide age-related cognitive decline and dementia. In the absence of effective therapeutic interventions, identifying risk factors associated with cognitive decline becomes increasingly vital. Novel perspectives suggest that a dynamic bidirectional communication system between the gut, its microbiome, and the central nervous system, commonly referred to as the microbiota-gut-brain axis, may be a contributing factor for cognitive health and disease. However, the exact mechanisms remain undefined. Microbial-derived metabolites produced in the gut can cross the intestinal epithelial barrier, enter systemic circulation and trigger physiological responses both directly and indirectly affecting the central nervous system and its functions. Dysregulation of this system (i.e., dysbiosis) can modulate cytotoxic metabolite production, promote neuroinflammation and negatively impact cognition. In this review, we explore critical connections between microbial-derived metabolites (secondary bile acids, trimethylamine-N-oxide (TMAO), tryptophan derivatives and others) and their influence upon cognitive function and neurodegenerative disorders, with a particular interest in their less-explored role as risk factors of cognitive decline.
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9
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Peddireddy KR, Michieletto D, Aguirre G, Garamella J, Khanal P, Robertson-Anderson RM. DNA Conformation Dictates Strength and Flocculation in DNA-Microtubule Composites. ACS Macro Lett 2021; 10:1540-1548. [PMID: 35549144 PMCID: PMC9239750 DOI: 10.1021/acsmacrolett.1c00638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polymer topology has been shown to play a key role in tuning the dynamics of complex fluids and gels. At the same time, polymer composites, ubiquitous in everyday life, have been shown to exhibit emergent desirable mechanical properties not attainable in single-species systems. Yet, how topology impacts the dynamics and structure of polymer composites remains poorly understood. Here, we create composites of rigid rods (microtubules) polymerized within entangled solutions of flexible linear and ring polymers (DNA) of equal length. We couple optical tweezers microrheology with confocal microscopy and scaled particle theory to show that composites with linear DNA exhibit a strongly nonmonotonic dependence of elasticity and stiffness on microtubule concentration due to depletion-driven polymerization and flocculation of microtubules. In contrast, composites containing ring DNA show a much more modest monotonic increase in elastic strength with microtubule concentration, which we demonstrate arises from the decreased conformational size and increased miscibility of rings.
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Affiliation(s)
- Karthik R Peddireddy
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, California 92110, United States
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gina Aguirre
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, California 92110, United States
| | - Jonathan Garamella
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, California 92110, United States
| | - Pawan Khanal
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, California 92110, United States
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, California 92110, United States
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10
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Mueed Z, Mehta D, Rai PK, Kamal MA, Poddar NK. Cross-Interplay between Osmolytes and mTOR in Alzheimer's Disease Pathogenesis. Curr Pharm Des 2021; 26:4699-4711. [PMID: 32418522 DOI: 10.2174/1381612826666200518112355] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease, categorized by the piling of amyloid-β (Aβ), hyperphosphorylated tau, PHFs, NFTs and mTOR hyperactivity, is a neurodegenerative disorder, affecting people across the globe. Osmolytes are known for osmoprotectants and play a pivotal role in protein folding, function and protein stability, thus, preventing proteins aggregation, and counteracting effects of denaturing solutes on proteins. Osmolytes (viz., sorbitol, inositol, and betaine) perform a pivotal function of maintaining homeostasis during hyperosmotic stress. The selective advantage of utilising osmolytes over inorganic ions by cells is in maintaining cell volume without compromising cell function, which is important for organs such as the brain. Osmolytes have been documented not only as neuroprotectors but they also seem to act as neurodegenerators. Betaine, sucrose and trehalose supplementation has been seen to induce autophagy thereby inhibiting the accumulation of Aβ. In contrast, sucrose has also been associated with mTOR hyperactivity, a hallmark of AD pathology. The neuroprotective action of taurine is revealed when taurine supplementation is seen to inhibit neural damage, apoptosis and oxidative damage. Inositol stereoisomers (viz., scyllo-inositol and myo-inositol) have also been seen to inhibit Aβ production and plaque formation in the brain, inhibiting AD pathogenesis. However, TMAO affects the aging process adversely by deregulating the mTOR signalling pathway and then kindling cognitive dysfunction via degradation of chemical synapses and synaptic plasticity. Thus, it can be concluded that osmolytes may act as a probable therapeutic approach for neurodevelopmental disorders. Here, we have reviewed and focussed upon the impact of osmolytes on mTOR signalling pathway and thereby its role in AD pathogenesis.
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Affiliation(s)
- Zeba Mueed
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Devanshu Mehta
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Pankaj K Rai
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Mohammad A Kamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia,Enzymoics; Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW 2770, Australia
| | - Nitesh K Poddar
- Department of Biosciences, Manipal University Jaipur, Rajasthan, India
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Association of Circulating Trimethylamine N-Oxide and Its Dietary Determinants with the Risk of Kidney Graft Failure: Results of the TransplantLines Cohort Study. Nutrients 2021; 13:nu13010262. [PMID: 33477634 PMCID: PMC7831477 DOI: 10.3390/nu13010262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Background. Due to the critical shortage of kidneys for transplantation, the identification of modifiable factors related to graft failure is highly desirable. The role of trimethylamine-N-oxide (TMAO) in graft failure remains undetermined. Here, we investigated the clinical utility of TMAO and its dietary determinants for graft failure prediction in renal transplant recipients (RTRs). Methods. We included 448 RTRs who participated in the TransplantLines Cohort Study. Cox proportional-hazards regression analyses were performed to study the association of plasma TMAO with graft failure. Net Benefit, which is a decision analysis method, was performed to evaluate the clinical utility of TMAO and dietary information in the prediction of graft failure. Results. Among RTRs (age 52.7 ± 13.1 years; 53% males), the baseline median TMAO was 5.6 (3.0–10.2) µmol/L. In multivariable regression analysis, the most important dietary determinants of TMAO were egg intake (Std. β = 0.09 [95%CI, 0.01; 0.18]; p = 0.03), fiber intake (Std. β = −0.14 [95%CI, −0.22, −0.05]; p = 0.002), and fish and seafood intake (Std. β = 0.12 [95%CI, 0.03,0.21]; p = 0.01). After a median follow-up of 5.3 (4.5–6.0) years, graft failure was observed in 58 subjects. TMAO was associated with an increased risk of graft failure, independent of age, sex, the body mass index (BMI), blood pressure, lipids, albuminuria, and the Estimated Glomerular Filtration Rate (eGFR) (Hazard Ratio per 1-SD increase of TMAO, 1.62 (95% confidence interval (CI): 1.22; 2.14, p < 0.001)). A TMAO and dietary enhanced prediction model offered approximately double the Net Benefit compared to a previously reported, validated prediction model for future graft failure, allowing the detection of 21 RTRs per 100 RTRs tested, with no false positives versus 10 RTRs, respectively. Conclusions. A predictive model for graft failure, enriched with TMAO and its dietary determinants, yielded a higher Net Benefit compared with an already validated model. This study suggests that TMAO and its dietary determinants are associated with an increased risk of graft failure and that it is clinically meaningful.
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13
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Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis. Sci Rep 2020; 10:9685. [PMID: 32546801 PMCID: PMC7297731 DOI: 10.1038/s41598-020-66710-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/20/2020] [Indexed: 12/24/2022] Open
Abstract
It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this paper, we propose to use the weighted persistent homology to systematically study the osmolytes molecular aggregation and their hydrogen-bonding network from a local topological perspective. We consider two weighted models, i.e., localized persistent homology (LPH) and interactive persistent homology (IPH). Boltzmann persistent entropy (BPE) is proposed to quantitatively characterize the topological features from LPH and IPH, together with persistent Betti number (PBN). More specifically, from the localized persistent homology models, we have found that TMAO and urea have very different local topology. TMAO is found to exhibit a local network structure. With the concentration increase, the circle elements in these networks show a clear increase in their total numbers and a decrease in their relative sizes. In contrast, urea shows two types of local topological patterns, i.e., local clusters around 6 Å and a few global circle elements at around 12 Å. From the interactive persistent homology models, it has been found that our persistent radial distribution function (PRDF) from the global-scale IPH has same physical properties as the traditional radial distribution function. Moreover, PRDFs from the local-scale IPH can also be generated and used to characterize the local interaction information. Other than the clear difference of the first peak value of PRDFs at filtration size 4 Å, TMAO and urea also shows very different behaviors at the second peak region from filtration size 5 Å to 10 Å. These differences are also reflected in the PBNs and BPEs of the local-scale IPH. These localized topological information has never been revealed before. Since graphs can be transferred into simplicial complexes by the clique complex, our weighted persistent homology models can be used in the analysis of various networks and graphs from any molecular structures and aggregation systems.
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14
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Swann JR, Spitzer SO, Diaz Heijtz R. Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Metabolites 2020; 10:metabo10050172. [PMID: 32344839 PMCID: PMC7281085 DOI: 10.3390/metabo10050172] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 01/23/2023] Open
Abstract
The gut microbiome is recognized to exert a wide-ranging influence on host health and disease, including brain development and behavior. Commensal bacteria can produce bioactive molecules that enter the circulation and impact host physiology and homeostasis. However, little is known about the potential for these metabolites to cross the blood–brain barrier and enter the developing brain under normal physiological conditions. In this study, we used a liquid chromatography–mass spectrometry-based metabolomic approach to characterize the developmental profiles of microbial-derived metabolites in the forebrains of mice across three key postnatal developmental stages, co-occurring with the maturation of the gut microbiota. We demonstrate that direct metabolites of the gut microbiome (e.g., imidazole propionate) or products of the combinatorial metabolism between the microbiome and host (e.g., 3-indoxyl-sulfate, trimethylamine-N-oxide, and phenylacetylglycine) are present in the forebrains of mice as early as the neonatal period and remain into adulthood. These findings demonstrate that microbial-associated molecules can cross the BBB either in their detected form or as precursor molecules that undergo further processing in the brain. These chemical messengers are able to bind receptors known to be expressed in the brain. Alterations in the gut microbiome may therefore influence neurodevelopmental trajectories via the regulation of these microbial-associated metabolites.
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Affiliation(s)
- Jonathan R. Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, University Road, Southampton SO17 1BJ, UK
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
- Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden
- Correspondence: (J.R.S.); (R.D.H.)
| | - Sonia O. Spitzer
- The Francis Crick Institute, London, 1 Midland Rd, London NW1 1AT, UK
| | - Rochellys Diaz Heijtz
- Department of Neuroscience, Karolinska Institute, 171 77 Stockholm, Sweden
- INSERM U1239, University of Rouen, Normandy, 76130 Mont-Saint-Aignan, France
- Correspondence: (J.R.S.); (R.D.H.)
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15
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Obrenovich M, Tabrez S, Siddiqui B, McCloskey B, Perry G. The Microbiota-Gut-Brain Axis-Heart Shunt Part II: Prosaic Foods and the Brain-Heart Connection in Alzheimer Disease. Microorganisms 2020; 8:E493. [PMID: 32244373 PMCID: PMC7232206 DOI: 10.3390/microorganisms8040493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/19/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023] Open
Abstract
There is a strong cerebrovascular component to brain aging, Alzheimer disease, and vascular dementia. Foods, common drugs, and the polyphenolic compounds contained in wine modulate health both directly and through the gut microbiota. This observation and novel findings centered on nutrition, biochemistry, and metabolism, as well as the newer insights we gain into the microbiota-gut-brain axis, now lead us to propose a shunt to this classic triad, which involves the heart and cerebrovascular systems. The French paradox and prosaic foods, as they relate to the microbiota-gut-brain axis and neurodegenerative diseases, are discussed in this manuscript, which is the second part of a two-part series of concept papers addressing the notion that the microbiota and host liver metabolism all play roles in brain and heart health.
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Affiliation(s)
- Mark Obrenovich
- Research Service, Louis Stokes Cleveland, Department of Veteran’s Affairs Medical Center, Cleveland, OH 44106, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- The Gilgamesh Foundation for Medical Science and Research, Cleveland, OH 44116, USA;
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606, USA
- Departments of Chemistry and Biological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bushra Siddiqui
- North East Ohio College of Medicine, Rootstown, OH 44272, USA;
| | - Benjamin McCloskey
- The Gilgamesh Foundation for Medical Science and Research, Cleveland, OH 44116, USA;
| | - George Perry
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
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16
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Hildre AS, Solvang SEH, Aarsland D, Midtun Ø, McCann A, Ervik AO, Nygård O, Ueland PM, Nordrehaug JE, Giil LM. Components of the choline oxidation pathway modify the association between the apolipoprotein ε4 gene variant and cognitive decline in patients with dementia. Brain Res 2019; 1726:146519. [PMID: 31654640 DOI: 10.1016/j.brainres.2019.146519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/12/2019] [Accepted: 10/19/2019] [Indexed: 11/18/2022]
Abstract
BACKGROUND Metabolites involved in one-carbon metabolism (OCM) may predict cognitive prognosis in dementia. The link between OCM, apolipoprotein E (APOE), and DNA methylation creates a biologically plausible mechanism of interaction. AIM To assess OCM metabolites as predictors of 5-year cognitive prognosis in patients with mild dementia, and in subgroups defined by the APOEε4 allele variant. METHODS We followed one-hundred and fifty-two patients with mild dementia (86 with Alzheimer's disease, 66 with Lewy body dementia, including 90 with at least one APOEε4 allele) for 5 years with annual Mini-Mental State Examinations (MMSE). Total homocysteine, methionine, choline, betaine, dimethylglycine, sarcosine, folate, cobalamin and pyridoxal 5'-phoshate were measured in serum at baseline. We used linear mixed models to assess metabolite-MMSE associations, including 3-way interactions between metabolites, time, and APOEε4. False-discovery rate adjusted p-values (Q-values) are reported. RESULTS Metabolite concentrations were not different in patients with dementia according to the presence of APOEε4. Overall, serum concentration of total homocysteine was inversely associated with MMSE performance, while betaine was positively associated with MMSE (Q < 0.05), but neither was associated with MMSE decline. Serum concentrations of betaine, dimethylglycine and sarcosine, however, were associated with slower MMSE decline in patients with APOEε4, but with faster MMSE decline in patients without the allele (all 3-way interactions: Q < 0.05). CONCLUSION Components of the choline oxidation pathway are associated with a better cognitive prognosis in APOEε4 carriers and a worse cognitive prognosis in non-carriers. Further research investigating targeted metabolic interventions according to APOE allele status is warranted.
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Affiliation(s)
| | - Stein-Erik Hafstad Solvang
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Dag Aarsland
- Department of Old Age Psychiatry, King's College University, London, UK
| | | | | | - Arne Olav Ervik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ottar Nygård
- Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | | | - Jan Erik Nordrehaug
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Lasse Melvaer Giil
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway.
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Parker A, Fonseca S, Carding SR. Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes 2019; 11:135-157. [PMID: 31368397 PMCID: PMC7053956 DOI: 10.1080/19490976.2019.1638722] [Citation(s) in RCA: 329] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
The human gastrointestinal (gut) microbiota comprises diverse and dynamic populations of bacteria, archaea, viruses, fungi, and protozoa, coexisting in a mutualistic relationship with the host. When intestinal homeostasis is perturbed, the function of the gastrointestinal tract and other organ systems, including the brain, can be compromised. The gut microbiota is proposed to contribute to blood-brain barrier disruption and the pathogenesis of neurodegenerative diseases. While progress is being made, a better understanding of interactions between gut microbes and host cells, and the impact these have on signaling from gut to brain is now required. In this review, we summarise current evidence of the impact gut microbes and their metabolites have on blood-brain barrier integrity and brain function, and the communication networks between the gastrointestinal tract and brain, which they may modulate. We also discuss the potential of microbiota modulation strategies as therapeutic tools for promoting and restoring brain health.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Sonia Fonseca
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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18
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Mukherjee M, Mondal J. Osmolyte-Induced Collapse of a Charged Macromolecule. J Phys Chem B 2019; 123:4636-4644. [DOI: 10.1021/acs.jpcb.9b01383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mrinmoy Mukherjee
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Jagannath Mondal
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
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19
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Moriizumi Y, Tabata KV, Miyoshi D, Noji H. Osmolyte-Enhanced Protein Synthesis Activity of a Reconstituted Translation System. ACS Synth Biol 2019; 8:557-567. [PMID: 30763512 DOI: 10.1021/acssynbio.8b00513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular crowding is receiving great attention in cell-free synthetic biology because molecular crowding is a critical feature of natural cell discrimination from artificial cells. Further, it has significant and generic influences on biomolecular functions. Although there are reports on how the macromolecular crowder reagents affect cell-free systems such as transcription and translation, the second class of molecular crowder reagents with low molecular weight, osmolyte, was much less studied in cell-free systems. In the present study, we focused on trimethylamine- N-oxide (TMAO) and betaine, methylamine osmolytes, and investigated the effectiveness of these osmolytes on gene expression activity of reconstituted cell-free protein synthesis. The gene expression activity of the fluorescent proteins Venus and tdTomato and the enzymes β-galactosidase and dihydrofolate reductase were tested. At 37 °C, 0.4 M TMAO showed the highest enhancement of translational activity by a factor of 1.6-3.8, regardless of protein type. In contrast, betaine showed only a moderate effect that was limited to fluorescent proteins. Excess amounts of osmolytes suppressed gene expression activity. An mRNA-start assay and SDS-PAGE quantitative analysis provided firm evidence that TMAO enhances the translation process, instead of transcription, folding, or the maturation of fluorescent proteins. Interestingly, at 26 °C, TMAO and betaine showed the highest enhancement of protein synthesis activity at lower concentrations than at 37 °C. These findings provide implications on how osmolytes assist translation in natural cells. Further, they provide guidelines for modulation of protein synthesis activity in artificial cells through osmolyte addition.
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Affiliation(s)
- Yoshiki Moriizumi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuhito V. Tabata
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daisuke Miyoshi
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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20
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Stasyuk N, Gayda G, Zakalskiy A, Zakalska O, Serkiz R, Gonchar M. Amperometric biosensors based on oxidases and PtRu nanoparticles as artificial peroxidase. Food Chem 2019; 285:213-220. [PMID: 30797337 DOI: 10.1016/j.foodchem.2019.01.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/03/2019] [Accepted: 01/22/2019] [Indexed: 12/23/2022]
Abstract
Catalytically active nanomaterials have several advantages over their natural analogues when used as artificial enzymes (nanozymes), namely, higher stability and lower cost. Nanozymes with metallic nanocomposites are promising catalysts for biosensing applications. The aim of the current research is to construct oxidase-based bioelectrodes for food analysis using nanozymes as peroxidase mimetics. Bimetallic PtRu nanoparticles (nPtRu) coupled with alcohol oxidase (AO) and methylamine oxidase (AMO) were chosen to construct amperometric biosensors (ABSs) for primary alcohols and methylamine (MA). Both ABSs show high sensitivities (336 A·M-1·m-2 for the AO-ABS and 284 A·M-1·m-2 for the AMO-ABS), broad linear ranges (25-200 µM ethanol and 20-600 µM MA) and satisfactory storage stabilities. Practical feasibility of the constructed ABSs was demonstrated on food samples. High correlation between contents of MA and ethanol in foods determined by the ABSs and reference methods was observed.
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Affiliation(s)
- Nataliya Stasyuk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Galina Gayda
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine.
| | - Andriy Zakalskiy
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Oksana Zakalska
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Roman Serkiz
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine; Ivan Franko National University of Lviv, Department of Solid State Physics, Drahomanov Street 50, 79005 Lviv, Ukraine
| | - Mykhailo Gonchar
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
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21
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Xia K, Anand DV, Shikhar S, Mu Y. Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks. Phys Chem Chem Phys 2019; 21:21038-21048. [DOI: 10.1039/c9cp03009c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.
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Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Saxena Shikhar
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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22
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Implication of Trimethylamine N-Oxide (TMAO) in Disease: Potential Biomarker or New Therapeutic Target. Nutrients 2018; 10:nu10101398. [PMID: 30275434 PMCID: PMC6213249 DOI: 10.3390/nu10101398] [Citation(s) in RCA: 385] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/12/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) is a molecule generated from choline, betaine, and carnitine via gut microbial metabolism. The plasma level of TMAO is determined by several factors including diet, gut microbial flora, drug administration and liver flavin monooxygenase activity. In humans, recent clinical studies evidence a positive correlation between elevated plasma levels of TMAO and an increased risk for major adverse cardiovascular events. A direct correlation between increased TMAO levels and neurological disorders has been also hypothesized. Several therapeutic strategies are being explored to reduce TMAO levels, including use of oral broad spectrum antibiotics, promoting the growth of bacteria that use TMAO as substrate and the development of target-specific molecules. Despite the accumulating evidence, it is questioned whether TMAO is the mediator of a bystander in the disease process. Thus, it is important to undertake studies to establish the role of TMAO in human health and disease. In this article, we reviewed dietary sources and metabolic pathways of TMAO, as well as screened the studies suggesting possible involvement of TMAO in the etiology of cardiovascular and neurological disorders, underlying the importance of TMAO mediating inflammatory processes. Finally, the potential utility of TMAO as therapeutic target is also analyzed.
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23
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Mukherjee M, Mondal J. Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction. J Phys Chem B 2018; 122:6922-6930. [DOI: 10.1021/acs.jpcb.8b04654] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mrinmoy Mukherjee
- Tata Institute of Fundamental Research Hyderabad, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Hyderabad 500107, India
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24
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Bachand GD, Jain R, Ko R, Bouxsein NF, VanDelinder V. Inhibition of Microtubule Depolymerization by Osmolytes. Biomacromolecules 2018; 19:2401-2408. [PMID: 29689154 DOI: 10.1021/acs.biomac.7b01799] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microtubule dynamics play a critical role in the normal physiology of eukaryotic cells as well as a number of cancers and neurodegenerative disorders. The polymerization/depolymerization of microtubules is regulated by a variety of stabilizing and destabilizing factors, including microtubule-associated proteins and therapeutic agents (e.g., paclitaxel, nocodazole). Here we describe the ability of the osmolytes polyethylene glycol (PEG) and trimethylamine- N-oxide (TMAO) to inhibit the depolymerization of individual microtubule filaments for extended periods of time (up to 30 days). We further show that PEG stabilizes microtubules against both temperature- and calcium-induced depolymerization. Our results collectively suggest that the observed inhibition may be related to combination of the kosmotropic behavior and excluded volume/osmotic pressure effects associated with PEG and TMAO. Taken together with prior studies, our data suggest that the physiochemical properties of the local environment can regulate microtubule depolymerization and may potentially play an important role in in vivo microtubule dynamics.
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Affiliation(s)
- George D Bachand
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Rishi Jain
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Randy Ko
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Nathan F Bouxsein
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Virginia VanDelinder
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
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25
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Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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26
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Tah I, Mondal J. How Does a Hydrophobic Macromolecule Respond to a Mixed Osmolyte Environment? J Phys Chem B 2016; 120:10969-10978. [DOI: 10.1021/acs.jpcb.6b08378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Indrajit Tah
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad, India
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27
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Yang Y, Mu Y, Li W. Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Phys Chem Chem Phys 2016; 18:22081-8. [DOI: 10.1039/c6cp01205a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.
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Affiliation(s)
- Yanmei Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
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28
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Rahman S, Warepam M, Singh LR, Dar TA. A current perspective on the compensatory effects of urea and methylamine on protein stability and function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:129-36. [PMID: 26095775 DOI: 10.1016/j.pbiomolbio.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/16/2022]
Abstract
Urea is a strong denaturant and inhibits many enzymes but is accumulated intracellularly at very high concentrations (up to 3-4 M) in mammalian kidney and in many marine fishes. It is known that the harmful effects of urea on the macromolecular structure and function is offset by the accumulation of an osmolytic agent called methylamine. Intracellular concentration of urea to methylamines falls in the ratio of 2:1 to 3:2 (molar ratio). At this ratio, the thermodynamic effects of urea and methylamines on protein stability and function are believed to be algebraically additive. The mechanism of urea-methylamine counteraction has been widely investigated on various approaches including, thermodynamic, structural and functional aspects. Recent advances have also revealed atomic level insights of counteraction and various molecular dynamic simulation studies have yielded significant molecular level informations on the interaction between urea and methylamines with proteins. It is worthwhile that urea-methylamine system not only plays pivotal role for the survival and functioning of the renal medullary cells but also is a key osmoregulatory component of the marine elasmobranchs, holocephalans and coelacanths. Therefore, it is important to combine all discoveries and discuss the developments in context to physiology of the mammalian kidney and adaptation of the marine organisms. In this article we have for the first time reviewed all major developments on urea-counteraction systems to date. We have also discussed about other additional urea-counteraction systems discovered so far including urea-NaCl, urea-myoinsoitol and urea-molecular chaperone systems. Insights for the possible future research have also been highlighted.
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Affiliation(s)
- Safikur Rahman
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Laishram R Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Tanveer Ali Dar
- Clinical Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India.
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29
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Ufnal M, Zadlo A, Ostaszewski R. TMAO: A small molecule of great expectations. Nutrition 2015; 31:1317-23. [PMID: 26283574 DOI: 10.1016/j.nut.2015.05.006] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/07/2015] [Accepted: 05/10/2015] [Indexed: 12/19/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a small organic compound whose concentration in blood increases after ingesting dietary l-carnitine and phosphatidylcholine. Recent clinical studies show a positive correlation between elevated plasma levels of TMAO and an increased risk for major adverse cardiovascular events defined as death, myocardial infarction, or stroke. Several experimental studies suggest a possible contribution of TMAO to the etiology of cardiovascular diseases by affecting lipid and hormonal homeostasis. On the other hand, TMAO-rich seafood, which is an important source of protein and vitamins in the Mediterranean diet, has been considered beneficial for the circulatory system. Although in humans TMAO is known mainly as a waste product of choline metabolism, a number of studies suggest an involvement of TMAO in important biological functions in numerous organisms, ranging from bacteria to mammals. For example, cells use TMAO to maintain cell volume under conditions of osmotic and hydrostatic pressure stresses. In this article, we reviewed well-established chemical and biological properties of TMAO and dietary sources of TMAO, as well as looked at the studies suggesting possible involvement of TMAO in the etiology of cardiovascular and other diseases, such as kidney failure, diabetes, and cancer.
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Affiliation(s)
- Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland.
| | - Anna Zadlo
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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30
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Samanta N, Mahanta DD, Hazra S, Kumar GS, Mitra RK. Short chain polyethylene glycols unusually assist thermal unfolding of human serum albumin. Biochimie 2014; 104:81-9. [DOI: 10.1016/j.biochi.2014.05.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
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Jain R, Sharma D, Kumar S, Kumar R. Factor Defining the Effects of Glycine Betaine on the Thermodynamic Stability and Internal Dynamics of Horse Cytochrome c. Biochemistry 2014; 53:5221-35. [DOI: 10.1021/bi500356c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rishu Jain
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Deepak Sharma
- Council
of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Sandeep Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Rajesh Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
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Methylamine-sensitive amperometric biosensor based on (His)6-tagged Hansenula polymorpha methylamine oxidase immobilized on the gold nanoparticles. BIOMED RESEARCH INTERNATIONAL 2014; 2014:480498. [PMID: 25136590 PMCID: PMC4124223 DOI: 10.1155/2014/480498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/02/2014] [Accepted: 06/20/2014] [Indexed: 11/23/2022]
Abstract
A novel methylamine-selective amperometric bienzyme biosensor based on recombinant primary amine oxidase isolated from the recombinant yeast strain Saccharomyces cerevisiae and commercial horseradish peroxidase is described. Two amine oxidase preparations were used: free enzyme (AMO) and covalently immobilized on the surface of gold nanoparticles (AMO-nAu). Some bioanalytical parameters (sensitivity, selectivity, and storage stability) of the developed biosensors were investigated. The sensitivity for both sensors is high: 1450 ± 113 and 700 ± 30 A−1·M−1·m−2 for AMO-nAu biosensor, respectively. The biosensors exhibit the linear range from 15 μM to 150 μM (AMO-nAu) and from 15 μM to 60 μM (AMO). The developed biosensor demonstrated a good selectivity toward methylamine (MA) (signal for dimethylamine and trimethylamine is less than 5% and for ethylamine 15% compared to MA output) and reveals a satisfactory storage stability. The constructed amperometric biosensor was used for MA assay in real samples of fish products in comparison with chemical method. The values obtained with both approaches different methods demonstrated a high correlation.
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Bioconversion of airborne methylamine by immobilized recombinant amine oxidase from the thermotolerant yeast Hansenula polymorpha. ScientificWorldJournal 2014; 2014:898323. [PMID: 24672387 PMCID: PMC3929277 DOI: 10.1155/2014/898323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/26/2013] [Indexed: 11/17/2022] Open
Abstract
Aliphatic amines, including methylamine, are air-pollutants, due to their intensive use in industry and the natural degradation of proteins, amino acids, and other nitrogen-containing compounds in biological samples. It is necessary to develop systems for removal of methylamine from the air, since airborne methylamine has a negative effect on human health. The primary amine oxidase (primary amine : oxygen oxidoreductase (deaminating) or amine oxidase, AMO; EC 1.4.3.21), a copper-containing enzyme from the thermotolerant yeast Hansenula polymorpha which was overexpressed in baker's yeast Saccharomyces cerevisiae, was tested for its ability to oxidize airborne methylamine. A continuous fluidized bed bioreactor (CFBR) was designed to enable bioconversion of airborne methylamine by AMO immobilized in calcium alginate (CA) beads. The results demonstrated that the bioreactor with immobilized AMO eliminates nearly 97% of the airborne methylamine. However, the enzymatic activity of AMO causes formation of formaldehyde. A two-step bioconversion process was therefore proposed. In the first step, airborne methylamine was fed into a CFBR which contained immobilized AMO. In the second step, the gas flow was passed through another CFBR, with alcohol oxidase from the yeast H. polymorpha immobilized in CA, in order to decompose the formaldehyde formed in the first step. The proposed system provided almost total elimination of the airborne methylamine and the formaldehyde.
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Mondal J, Stirnemann G, Berne BJ. When does trimethylamine N-oxide fold a polymer chain and urea unfold it? J Phys Chem B 2013; 117:8723-32. [PMID: 23800089 DOI: 10.1021/jp405609j] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N-oxide (TMAO) that favors protein folding and the denaturing osmolyte urea are addressed by studying their effects on the folding of uncharged polymer chains. Using atomistic molecular dynamics simulations, we show that 1 M TMAO and 7 M urea solutions act dramatically differently on these model polymer chains. Their behaviors are sensitive to the strength of the attractive dispersion interactions of the chain with its environment: when these dispersion interactions are sufficiently strong, TMAO suppresses the formation of extended conformations of the hydrophobic polymer as compared to water while urea promotes the formation of extended conformations. Similar trends are observed experimentally for real protein systems. Quite surprisingly, we find that both protecting and denaturing osmolytes strongly interact with the polymer, seemingly in contrast with existing explanations of the osmolyte effect on proteins. We show that what really matters for a protective osmolyte is its effective depletion as the polymer conformation changes, which leads to a negative change in the preferential binding coefficient. For TMAO, there is a much more favorable free energy of insertion of a single osmolyte near collapsed conformations of the polymer than near extended conformations. By contrast, urea is preferentially stabilized next to the extended conformation and thus has a denaturing effect.
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Affiliation(s)
- Jagannath Mondal
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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Huang C, Lei H, Zhao X, Tang H, Wang Y. Metabolic influence of acute cyadox exposure on Kunming mice. J Proteome Res 2012; 12:537-45. [PMID: 23234330 DOI: 10.1021/pr301033a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cyadox is an antibiotic drug and has the potential to be used as a feedstuff additive in promoting the growth of animals. However, the toxicity of cyadox should be fully assessed before application, and this has prompted the current investigation on the metabolic responses of mice to cyadox exposure, using a metabonomic technique. Three groups of Kunming mice were respectively given a single dose of cyadox at three different concentrations (100, 650, and 4000 mg/kg body weight) via gavage. We present here the metabolic alterations of urine, plasma, liver, and renal medulla extracts induced by cyadox exposure. The metabolic alterations induced by cyadox exposure are dose-dependent, and metabolic recovery is achieved only for low and moderate levels of cyadox exposure during the experimental period. Cyadox exposure resulted in a disturbance of gut microbiota, which is manifested in depleted levels of urinary hippurate, trimethylamine-N-oxide (TMAO), dimethylamine (DMA), and trimethylamine (TMA). In addition, mice exposed to cyadox at high levels caused accumulations of amino acids and depletions of nucleotides in the liver. Furthermore, marked elevations of nucleotides and a range of organic osmolytes, such as myo-inositol, choline, and glycerophosphocholine (GPC), and decreased levels of amino acids are observed in the renal medulla of cyadox-exposed mice. These results suggest that cyadox exposure causes inhibition of amino acid metabolism in the liver and disturbance of gut microbiota community, influencing osmolytic homeostasis and nucleic acids synthesis in both the liver and the kidney. Our work provides a comprehensive view of the toxicological effects of cyadox, which is important in animal and human food safety.
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Affiliation(s)
- Chongyang Huang
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
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36
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Ascione G, de Pascale D, De Santi C, Pedone C, Dathan NA, Monti SM. Native expression and purification of hormone-sensitive lipase from Psychrobacter sp. TA144 enhances protein stability and activity. Biochem Biophys Res Commun 2012; 420:542-6. [DOI: 10.1016/j.bbrc.2012.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/07/2012] [Indexed: 11/25/2022]
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Sibirny V, Demkiv O, Klepach H, Honchar T, Gonchar M. Alcohol oxidase- and formaldehyde dehydrogenase-based enzymatic methods for formaldehyde assay in fish food products. Food Chem 2011; 127:774-9. [DOI: 10.1016/j.foodchem.2010.12.146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 10/21/2010] [Accepted: 12/31/2010] [Indexed: 11/16/2022]
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38
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Hu CY, Lynch GC, Kokubo H, Pettitt BM. Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model. Proteins 2010; 78:695-704. [PMID: 19790265 DOI: 10.1002/prot.22598] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of organic osmolytes has been pivotal in demonstrating the role of solvent effects on the protein backbone in the folding process. Although a thermodynamic description of the interactions between the protein backbone and osmolyte has been well defined, the structural analysis of the effect of osmolyte on the protein backbone has been incomplete. Therefore, we have performed simulations of a peptide backbone model, glycine(15), in protecting osmolyte trimethylamine N-oxide (TMAO) solution, in order to determine the effect of the solution structure on the conformation of the peptide backbone. We show that the models chosen show that the ensemble of backbone structures shifts toward a more collapsed state in TMAO solution as compared with pure water solution. The collapse is consistent with preferential exclusion of the osmolyte caused by unfavorable interactions between osmolyte and peptide backbone. The exclusion is caused by strong triplet correlations of osmolyte, water, and peptide backbone. This provides a clear mechanism showing that even a modest concentration of TMAO forces the protein backbone to adopt a more collapsed structure in the absence of side chain effects.
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Affiliation(s)
- Char Y Hu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA
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39
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The enhancement effect of beta-boswellic acid on hippocampal neurites outgrowth and branching (an in vitro study). Neurol Sci 2010; 31:315-20. [DOI: 10.1007/s10072-010-0220-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
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40
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Yancey P, Heppenstall M, Ly S, Andrell R, Gates R, Carter V, Hagedorn M. Betaines and Dimethylsulfoniopropionate as Major Osmolytes in Cnidaria with Endosymbiotic Dinoflagellates. Physiol Biochem Zool 2010; 83:167-73. [DOI: 10.1086/644625] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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41
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Wang DL, Wang XS, Xiao R, Liu Y, He RQ. Tubulin assembly is disordered in a hypogeomagnetic field. Biochem Biophys Res Commun 2008; 376:363-8. [DOI: 10.1016/j.bbrc.2008.08.156] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 08/28/2008] [Indexed: 11/25/2022]
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42
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Studying the Structure of Microtubules by Electron Microscopy. METHODS IN MOLECULAR MEDICINE™ 2007; 137:65-91. [DOI: 10.1007/978-1-59745-442-1_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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43
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Hovagimyan KG, Gerig JT. Interactions of TrimethylamineN−Oxide and Water withcyclo-Alanylglycine. J Phys Chem B 2005; 109:24142-51. [PMID: 16375406 DOI: 10.1021/jp055075+] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The osmolyte trimethylamine N-oxide (TMAO) is one of a family of compounds found in living systems that can stabilize biomolecular tertiary structures. As a step in exploring the interactions between this material and polyamino acids, we have determined intermolecular 1H{1H} nuclear Overhauser effects (NOEs) between the protons of cyclo-alanylglycine and protons of solvent components in TMAO-water solutions. Comparison of the results to effects predicted on the basis of the molecular shape of the dipeptide and experimental translational diffusion coefficients suggests that both water and TMAO molecules have properties in the vicinity of the dipeptide that are different from those in the bulk solution. Changes of local concentrations of water and TMAO and changes in the diffusive behavior of these components near the dipeptide are rejected as possible explanations of the discrepancies between observed and calculated Overhauser effects. Rather, it is concluded that TMAO molecules, and the water molecules associated with them, participate to some extent in the formation of long-lived solute-solvent complexes. The aliphatic alcohol tert-butyl alcohol is structurally similar to TMAO. Overhauser effect studies of its interaction with cyclo-alanylglycine in tert-butyl alcohol-water suggest similar kinds of interactions are present in this system but that they are significantly weaker, presumably because of the lower polarity of this alcohol compared to TMAO.
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Affiliation(s)
- Karen G Hovagimyan
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, USA
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44
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Doucet C, Dutheil D, Petit I, Zhang K, Eugene M, Touchard G, Wahl A, Seguin F, Milinkevitch S, Hauet T, Mauco G. Influence of colloid, preservation medium and trimetazidine on renal medulla injury. Biochim Biophys Acta Gen Subj 2004; 1673:105-14. [PMID: 15279881 DOI: 10.1016/j.bbagen.2004.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 03/01/2004] [Accepted: 03/31/2004] [Indexed: 12/14/2022]
Abstract
In organ transplantation, preservation injury is an important factor which could influence short-term and long-term graft outcome. The renal medulla is particularly sensitive to oxidant stress and ischemia-reperfusion injury (IRI). Using an autotransplant pig kidney model, we investigated renal function and medullary damage determined between day 1 and week 2 after 24- or 48-h cold storage in different preservation solutions: University of Wisconsin solution (UW), Hopital Edouard Herriot solution (a high Na+ version of UW), ECPEG (high Na+ preservation solution with PEG) and ICPEG (a high K+ version of ECPEG) with or without trimetazidine (TMZ). TMZ improved renal preservation and increased renal function when added in each preservation solution (particularly HEH and ECPEG). Medullary damage led to the early appearance of trimethylamine-N-oxide (TMAO) followed by 1H-NMR in urine and plasma. TMZ and ECPEG is the most efficient association to reduce medullary damage. This study clarifies the role of colloid and polarity solution and the role of mitochondrial protection by TMZ.
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Affiliation(s)
- Carole Doucet
- INSERM ERM 324, Rue de La Milétrie, CHU de Poitiers, 86000, Poitiers, France
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45
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Faure JP, Jayle C, Dutheil D, Eugene M, Zhang K, Goujon JM, Petit-Paris I, Tillement JP, Touchard G, Robert R, Wahl A, Seguin F, Mauco G, Vandewalle A, Hauet T. Evidence for protective roles of polyethylene glycol plus high sodium solution and trimetazidine against consequences of renal medulla ischaemia during cold preservation and reperfusion in a pig kidney model. Nephrol Dial Transplant 2004; 19:1742-51. [PMID: 15128878 DOI: 10.1093/ndt/gfh142] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The renal medulla is particularly sensitive to oxidant stress and to ischaemia-reperfusion injury (IRI). In organ transplantation, delayed graft function is an important problem and cold ischaemia is thought to be the most important factor in short- and long-term complications. Our aim was to study cold-induced damage in proximal tubular segments and renal medulla osmolite excretion during use of various preservation solutions, and to clarify the role of trimetazidine (TMZ) in limiting renal dysfunction. METHODS Using an autotransplanted pig kidney model, we assessed renal tubule function, medullary osmolite excretion and renal damage between day 1 and week 2 after 24 or 48 h cold storage in University of Wisconsin solution (UW), Celsior and ECPEG (two new high Na(+) preservation solutions) or the Hopital Edouard Herriot solution (HEH; a high Na(+) version of UW). In additional groups, TMZ was added to these preservation solutions for 24 and 48 h cold storage. RESULTS Renal function was reduced under these preservation conditions. Tubular injury was associated with aminoaciduria and with a limited Na(+) reabsorbtion. Medullary damage led to the early appearance of trimethylamine-N-oxide and dimethylamine in urine. However, renal damage was modulated by preservation conditions. In addition, TMZ added to each of the solutions efficiently protected against IRI even after prolonged preservation. CONCLUSION TMZ efficiently protected kidneys against damage when added to the HEH and particularly ECPEG solutions, even after 24 h cold storage. These findings point to a role for drugs that target mitochondria, and demonstrate that TMZ may provide a valuable therapeutic tool against IRI and could be included in therapeutic protocols.
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Affiliation(s)
- Jean Pierre Faure
- INSERM ERM Poitiers, Département de Génétique Animale, Hôpital Jean Bernard, Poitiers, France
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46
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Bennion BJ, Daggett V. Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution. Proc Natl Acad Sci U S A 2004; 101:6433-8. [PMID: 15096583 PMCID: PMC404062 DOI: 10.1073/pnas.0308633101] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Accepted: 03/17/2004] [Indexed: 11/18/2022] Open
Abstract
Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.
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Affiliation(s)
- Brian J Bennion
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA
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47
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Kar S, Florence GJ, Paterson I, Amos LA. Discodermolide interferes with the binding of tau protein to microtubules. FEBS Lett 2003; 539:34-6. [PMID: 12650922 DOI: 10.1016/s0014-5793(03)00181-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We investigated whether discodermolide, a novel antimitotic agent, affects the binding to microtubules of tau protein repeat motifs. Like taxol, the new drug reduces the proportion of tau that pellets with microtubules. Despite their differing structures, discodermolide, taxol and tau repeats all bind to a site on beta-tubulin that lies within the microtubule lumen and is crucial in controlling microtubule assembly. Low concentrations of tau still bind strongly to the outer surfaces of preformed microtubules when the acidic C-terminal regions of at least six tubulin dimers are available for interaction with each tau molecule; otherwise binding is very weak.
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Affiliation(s)
- Santwana Kar
- MRC Laboratory of Molecular Biology, Hills Rd, Cambridge CB2 2QH, UK
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48
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Kar S, Fan J, Smith MJ, Goedert M, Amos LA. Repeat motifs of tau bind to the insides of microtubules in the absence of taxol. EMBO J 2003; 22:70-7. [PMID: 12505985 PMCID: PMC140040 DOI: 10.1093/emboj/cdg001] [Citation(s) in RCA: 246] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The tau family of microtubule-associated proteins has a microtubule-binding domain which includes three or four conserved sequence repeats. Pelleting assays show that when tubulin and tau are co- assembled into microtubules, the presence of taxol reduces the amount of tau incorporated. In the absence of taxol, strong binding sites for tau are filled by one repeat motif per tubulin dimer; additional tau molecules bind more weakly. We have labelled a repeat motif with nanogold and used three-dimensional electron cryomicroscopy to compare images of microtubules assembled with labelled or unlabelled tau. With kinesin motor domains bound to the microtubule outer surface to distinguish between alpha- and beta-tubulin, we show that the gold label lies on the inner surface close to the taxol binding site on beta-tubulin. Loops within the repeat motifs of tau have sequence similarity to an extended loop which occupies a site in alpha-tubulin equivalent to the taxol-binding pocket in beta-tubulin. We propose that loops in bound tau stabilize microtubules in a similar way to taxol, although with lower affinity so that assembly is reversible.
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Affiliation(s)
| | | | | | | | - Linda A. Amos
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Corresponding author e-mail:
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Abstract
Despite earlier uncertainties about the role of tau pathology in AD, the discovery of multiple mutations in the tau gene that lead to the abnormal aggregation of tau and the onset/progression of FTDP-17 demonstrates that tau dysfunction is sufficient to produce neurodegenerative disease. The mutations lead to specific cellular alterations, including altered expression, function and biochemistry of tau. The finding that specific tau gene mutations lead to diverse FTDP-17 phenotypes raises the possibility that the clinical and pathological expression of hereditary and related sporadic tauopathies may be influenced by tau gene polymorphisms, other genetic factors and epigenetic events. However, the precise mechanisms whereby tau assembles into filaments and causes neurodegeneration in the human brain remain to be elucidated, but further investigation into the mechanisms of tau dysfunction, as well as the identification of potential disease-modifying factors, will provide additional insight into novel strategies for the treatment and prevention of AD and related disorders. Moreover, development of additional animal models of tauopathies that more closely recapitulate human diseases will facilitate this undertaking, and this is likely to have implications for other neurodegenerative disorders since the aggregation of tau in AD and and related tauopathies is an example of abnormal protein-protein interactions resulting in the intracellular accumulation of filamentous proteins that is a common feature of many fatal CNS diseases characterized by relentlessly progressive brain degeneration [1-3]. Thus, the fibrillization and aggregation of proteins in the brain is a common theme in a diverse group of neurodegenerative disorders and insight into the pathogenesis of any one of these disorders may have implications for understanding the mechanisms that underlie all these diseases as well as for the discovery of better strategies to treat them [1-3].
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Affiliation(s)
- John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Maloney Building, 3rd Floor, HUP, Philadelphia, PA 19104, USA.
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50
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Abstract
The defining neuropathological characteristics of Alzheimer's disease are abundant filamentous tau lesions and deposits of fibrillar amyloid beta peptides. Prominent filamentous tau inclusions and brain degeneration in the absence of beta-amyloid deposits are also hallmarks of neurodegenerative tauopathies exemplified by sporadic corticobasal degeneration, progressive supranuclear palsy, and Pick's disease, as well as by hereditary frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). Because multiple tau gene mutations are pathogenic for FTDP-17 and tau polymorphisms appear to be genetic risk factors for sporadic progressive supranuclear palsy and corticobasal degeneration, tau abnormalities are linked directly to the etiology and pathogenesis of neurodegenerative disease. Indeed, emerging data support the hypothesis that different tau gene mutations are pathogenic because they impair tau functions, promote tau fibrillization, or perturb tau gene splicing, thereby leading to formation of biochemically and structurally distinct aggregates of tau. Nonetheless, different members of the same kindred often exhibit diverse FTDP-17 syndromes, which suggests that additional genetic or epigenetic factors influence the phenotypic manifestations of neurodegenerative tauopathies. Although these and other hypothetical mechanisms of neurodegenerative tauopathies remain to be tested and validated, transgenic models are increasingly available for this purpose, and they will accelerate discovery of more effective therapies for neurodegenerative tauopathies and related disorders, including Alzheimer's disease.
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Affiliation(s)
- V M Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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